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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NRXN1-NRXN1 (FusionGDB2 ID:HG9378TG9378)

Fusion Gene Summary for NRXN1-NRXN1

check button Fusion gene summary
Fusion gene informationFusion gene name: NRXN1-NRXN1
Fusion gene ID: hg9378tg9378
HgeneTgene
Gene symbol

NRXN1

NRXN1

Gene ID

9378

9378

Gene nameneurexin 1neurexin 1
SynonymsHs.22998|PTHSL2|SCZD17Hs.22998|PTHSL2|SCZD17
Cytomap('NRXN1')('NRXN1')

2p16.3

2p16.3

Type of geneprotein-codingprotein-coding
Descriptionneurexin-1neurexin Ineurexin-1neurexin I
Modification date2020032020200320
UniProtAcc

P58400

P58400

Ensembl transtripts involved in fusion geneENST00000331040, ENST00000342183, 
ENST00000401669, ENST00000401710, 
ENST00000402717, ENST00000404971, 
ENST00000405472, ENST00000405581, 
ENST00000406316, ENST00000406859, 
ENST00000342183, ENST00000401669, 
ENST00000401710, ENST00000402717, 
ENST00000404971, ENST00000405472, 
ENST00000406316, ENST00000406859, 
ENST00000331040, ENST00000405581, 
Fusion gene scores* DoF score7 X 7 X 1=498 X 8 X 5=320
# samples 79
** MAII scorelog2(7/49*10)=0.514573172829758
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NRXN1 [Title/Abstract] AND NRXN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNRXN1(51256112)-NRXN1(50170866), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ABX487736NRXN1chr2

51256112

-NRXN1chr2

50170866

-


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Fusion Gene ORF analysis for NRXN1-NRXN1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000331040ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000331040ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000342183ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401669ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000401710ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000402717ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000404971ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405472ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000405581ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406316ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000342183NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000401669NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000401710NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000402717NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000404971NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000405472NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000406316NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-3CDSENST00000406859ENST00000406859NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000331040ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000331040ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000342183ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000342183ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000401669ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000401669ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000401710ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000401710ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000402717ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000402717ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000404971ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000404971ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000405472ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000405472ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000405581ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000405581ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000406316ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000406316ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000406859ENST00000331040NRXN1chr2

51256112

-NRXN1chr2

50170866

-
intron-intronENST00000406859ENST00000405581NRXN1chr2

51256112

-NRXN1chr2

50170866

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for NRXN1-NRXN1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for NRXN1-NRXN1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:51256112/:50170866)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NRXN1

P58400

NRXN1

P58400

FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion by forming intracellular junctions through binding to neuroligins. May play a role in formation or maintenance of synaptic junctions. May mediate intracellular signaling. May play a role in angiogenesis (By similarity). {ECO:0000250}.FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion by forming intracellular junctions through binding to neuroligins. May play a role in formation or maintenance of synaptic junctions. May mediate intracellular signaling. May play a role in angiogenesis (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NRXN1-NRXN1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NRXN1-NRXN1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for NRXN1-NRXN1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NRXN1-NRXN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNRXN1C0004352Autistic Disorder4CTD_human;GENOMICS_ENGLAND
HgeneNRXN1C0036341Schizophrenia3CTD_human
HgeneNRXN1C0005586Bipolar Disorder2PSYGENET
HgeneNRXN1C0020796Profound Mental Retardation2CTD_human
HgeneNRXN1C0025363Mental Retardation, Psychosocial2CTD_human
HgeneNRXN1C0917816Mental deficiency2CTD_human
HgeneNRXN1C3714756Intellectual Disability2CTD_human
HgeneNRXN1C0000772Multiple congenital anomalies1CTD_human
HgeneNRXN1C0011570Mental Depression1PSYGENET
HgeneNRXN1C0011581Depressive disorder1PSYGENET
HgeneNRXN1C0023012Language Delay1CTD_human
HgeneNRXN1C0023014Language Development Disorders1CTD_human
HgeneNRXN1C0241210Speech Delay1CTD_human
HgeneNRXN1C0376634Craniofacial Abnormalities1CTD_human
HgeneNRXN1C0454655Semantic-Pragmatic Disorder1CTD_human
HgeneNRXN1C0751257Auditory Processing Disorder, Central1CTD_human
HgeneNRXN1C1510586Autism Spectrum Disorders1CTD_human
HgeneNRXN1C1970431PITT-HOPKINS SYNDROME1CTD_human
HgeneNRXN1C3280479PITT-HOPKINS-LIKE SYNDROME 21CTD_human;GENOMICS_ENGLAND
TgeneC0004352Autistic Disorder4CTD_human;GENOMICS_ENGLAND
TgeneC0036341Schizophrenia3CTD_human
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC0020796Profound Mental Retardation2CTD_human
TgeneC0025363Mental Retardation, Psychosocial2CTD_human
TgeneC0917816Mental deficiency2CTD_human
TgeneC3714756Intellectual Disability2CTD_human
TgeneC0000772Multiple congenital anomalies1CTD_human
TgeneC0011570Mental Depression1PSYGENET
TgeneC0011581Depressive disorder1PSYGENET
TgeneC0023012Language Delay1CTD_human
TgeneC0023014Language Development Disorders1CTD_human
TgeneC0241210Speech Delay1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0454655Semantic-Pragmatic Disorder1CTD_human
TgeneC0751257Auditory Processing Disorder, Central1CTD_human
TgeneC1510586Autism Spectrum Disorders1CTD_human
TgeneC1970431PITT-HOPKINS SYNDROME1CTD_human
TgeneC3280479PITT-HOPKINS-LIKE SYNDROME 21CTD_human;GENOMICS_ENGLAND